getAnnotation: Downloading or Importing of Annotation Data

In fischuu/hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

Downloading or Importing of Annotation Data

Description

This function downloads (if needed) the annotation file from a given species from NCBI and loads it into the namespace.

Usage

  getAnnotation(species=NULL, assembly=NULL, annotationFolder=NULL, 
                type="gff3", verbose)

Arguments

species	The scientific name of the species (String).
assembly	The NCBI assembly version.
annotationFolder	The folder where the file will be stored.
type	The file extension/format of the annotation file.
verbose	Logical, if function gives feedback.

Details

This function downloads for a given species the annotation file, as provided from NCBI. The main parameters basically define the URL, where the file is located. The file is then downloaded into the folder, provided in annotationFolder and then imported to the namespace.

If a file has been downloaded previously, it will be loaded directly from that folder. In case the user wants to use an annotation that is not provided by NCBI, the corresponding files can also be placed into the same folder, following the naming scheme as suggested from the function and the function will load it from there.

Value

A data.table with the annotation information.

Author(s)

Daniel Fischer

Examples

## Not run: 
susScrofa <- getAnnotation(species = "Sus scrofa", 
                           annotationFolder="/home/user/annotation")
                           
homoSapiens <- getAnnotation(species = "Homo sapiens", 
                             annotationFolder="/home/user/annotation")

## End(Not run)

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.